From ff7110028b14758e8042ccd46ca5d89173ea00a7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 11 Jan 2020 19:16:34 -0500 Subject: [PATCH] make doc of pair style mm3/switch3/coulgauss/long consistent and complete --- doc/src/Commands_pair.rst | 2 +- ...st => pair_mm3_switch3_coulgauss_long.rst} | 2 +- doc/src/pair_style.rst | 2 +- doc/txt/pair_mm3_switch3_coulgauss.txt | 88 ------------------- 4 files changed, 3 insertions(+), 91 deletions(-) rename doc/src/{pair_mm3_switch3_coulgauss.rst => pair_mm3_switch3_coulgauss_long.rst} (98%) delete mode 100644 doc/txt/pair_mm3_switch3_coulgauss.txt diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 757a676c16..eaf0e680a0 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -176,6 +176,7 @@ OPT. * :doc:`meam/sw/spline ` * :doc:`mgpt ` * :doc:`mie/cut (g) ` + * :doc:`mm3/switch3/coulgauss/long ` * :doc:`momb ` * :doc:`morse (gkot) ` * :doc:`morse/smooth/linear (o) ` @@ -249,4 +250,3 @@ OPT. * :doc:`yukawa/colloid (go) ` * :doc:`zbl (gko) ` * - * diff --git a/doc/src/pair_mm3_switch3_coulgauss.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst similarity index 98% rename from doc/src/pair_mm3_switch3_coulgauss.rst rename to doc/src/pair_mm3_switch3_coulgauss_long.rst index c124b9b9b8..3f3a7cbc72 100644 --- a/doc/src/pair_mm3_switch3_coulgauss.rst +++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst @@ -37,7 +37,7 @@ Examples Description """"""""""" -The *mm3/switch3/coulgauss* style evaluates the MM3 +The *mm3/switch3/coulgauss/long* style evaluates the MM3 vdW potential :ref:`(Allinger) ` .. image:: Eqs/pair_mm3_switch3.jpg diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index f6f686fc12..db3056ed64 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -245,7 +245,7 @@ accelerated styles exist. * :doc:`meam/sw/spline ` - splined version of MEAM with a Stillinger-Weber term * :doc:`mgpt ` - simplified model generalized pseudopotential theory (MGPT) potential * :doc:`mie/cut ` - Mie potential -* `mm3/switch3/coulgauss `_ - smoothed MM3 vdW potential with Gaussian electrostatics +* :doc:`mm3/switch3/coulgauss/long `_ - smoothed MM3 vdW potential with Gaussian electrostatics * :doc:`momb ` - Many-Body Metal-Organic (MOMB) force field * :doc:`morse ` - Morse potential * :doc:`morse/smooth/linear ` - linear smoothed Morse potential diff --git a/doc/txt/pair_mm3_switch3_coulgauss.txt b/doc/txt/pair_mm3_switch3_coulgauss.txt deleted file mode 100644 index 86e6a0d1d9..0000000000 --- a/doc/txt/pair_mm3_switch3_coulgauss.txt +++ /dev/null @@ -1,88 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style mm3/switch3/coulgauss/long command :h3 - -[Syntax:] - -pair_style style args :pre - -style = {mm3/switch3/coulgauss/long} -args = list of arguments for a particular style :ul - {mm3/switch3/coulgauss/long} args = cutoff (cutoff2) width - cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - width = width parameter of the smoothing function (distance units) :pre - -[Examples:] - -pair_style mm3/switch3/coulgauss/long 12.0 3.0 -pair_coeff 1 0.2 2.5 1.2 :pre - -pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0 -pair_coeff 1 0.2 2.5 1.2 :pre - -[Description:] - -The {mm3/switch3/coulgauss} style evaluates the MM3 -vdW potential "(Allinger)"_#mm3-allinger1989 - -:c,image(Eqs/pair_mm3_switch3.jpg) - -, which goes smoothly to zero at the cutoff r_c as defined -by the switching function - -:c,image(Eqs/pair_switch3.jpg) - -where w is the width defined in the arguments. This potential -is combined with Coulomb interaction between Gaussian charge densities: - -:c,image(Eqs/pair_coulgauss.jpg) - -where qi and qj are the -charges on the 2 atoms, epsilon is the dielectric constant which -can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j -are the widths of the Gaussian charge distribution and erf() is the error-function. -This style has to be used in conjunction with the "kspace_style"_kspace_style.html command - -If one cutoff is specified it is used for both the vdW and Coulomb -terms. If two cutoffs are specified, the first is used as the cutoff -for the vdW terms, and the second is the cutoff for the Coulombic term. - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -epsilon (energy) -r_v (distance) -gamma (distance) :ul - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -Mixing rules are fixed for this style as defined above. - -Shifting the potential energy is not necessary because the switching -function ensures that the potential is zero at the cut-off. - - -[Restrictions:] - -These styles are part of the USER-YAFF package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none -